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Bendixen KK, Forsberg-Pho S, Dazio G, Hansen EE, Eriksen SK, Epistolio S, Merlo E, Boldorini R, Venesio T, Movilia A, Caprera C, Arnspang EC, Børgesen M, Christensen UB, Frattini M, Petersen RK. One-instrument, objective microsatellite instability analysis using high-resolution melt. PLoS One 2024; 19:e0302274. [PMID: 38662796 PMCID: PMC11045061 DOI: 10.1371/journal.pone.0302274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/29/2024] [Indexed: 04/28/2024] Open
Abstract
In recent years, immune checkpoint inhibitors have proved immense clinical progression in the treatment of certain cancers. The efficacy of immune checkpoint inhibitors is correlated with mismatch repair system deficiency and is exceptionally administered based exclusively on this biological mechanism independent of the cancer type. The promising effect of immune checkpoint inhibitors has left an increasing demand for analytical tools evaluating the mismatch repair status. The analysis of microsatellite instability (MSI), reflecting an indirect but objective manner the inactivation of the mismatch repair system, plays several roles in clinical practice and, therefore, its evaluation is of high relevance. Analysis of MSI by PCR followed by fragment analysis on capillary electrophoresis remains the gold standard method for detection of a deficient mismatch repair system and thereby treatment with immune checkpoint inhibitors. Novel technologies have been applied and concepts such as tumor mutation burden have been introduced. However, to date, most of these technologies require high costs or the need of matched non-tumor tissue as internal comparator. In this study, we present a novel, one-instrument, fast, and objective method for the detection of MSI (MicroSight® MSI 1-step HRM Analysis), which does not depend on the use of matched non-tumor tissue. The assay analyzes five well-described mononucleotide microsatellite sequences by real-time PCR followed by high-resolution melt and evaluates microsatellite length variations via PCR product melting profiles. The assay was evaluated using two different patient cohorts and evaluation included several DNA extraction methodologies, two different PCR platforms, and an inter-laboratory ring study. The MicroSight® MSI assay showed a high repeatability regardless of DNA extraction method and PCR platform, and a 100% agreement of the MSI status with PCR fragment analysis methods applied as clinical comparator.
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Affiliation(s)
| | | | - Giulia Dazio
- Institute of Pathology, Ente Ospedaliero Cantonale, Locarno, Switzerland
| | | | | | - Samantha Epistolio
- Institute of Pathology, Ente Ospedaliero Cantonale, Locarno, Switzerland
| | - Elisabetta Merlo
- Institute of Pathology, Ente Ospedaliero Cantonale, Locarno, Switzerland
| | - Renzo Boldorini
- Unit of Pathology, Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | - Tiziana Venesio
- Candiolo Cancer Institute, Fondazione del Piemonte per l’Oncologia, Candiolo, Italy
| | - Alessandra Movilia
- Hospital of Legnano, SS Biologia Molecolare, UO Anatomia Patologica, Azienda Socio Sanitaria Territoriale Ovest Milanese, Ospedale di Legnano, Legnano, Italy
| | - Cecilia Caprera
- Laboratory of Molecular Oncology and Predictive Medicine, Pathology Unit, Azienda Ospedaliera Santa Maria di Terni, Terni, Italy
| | - Eva Christensen Arnspang
- Department of Green Technology, Faculty of Engineering, University of Southern Denmark, Odense, Denmark
| | | | | | - Milo Frattini
- Institute of Pathology, Ente Ospedaliero Cantonale, Locarno, Switzerland
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Epistolio S, Dazio G, Zaed I, Sahnane N, Cipriani D, Polinelli F, Barizzi J, Spina P, Stefanini FM, Cerati M, Balbi S, Mazzucchelli L, Sessa F, Pesce GA, Reinert M, Cardia A, Marchi F, Frattini M. Clinical Relevance and Interplay between miRNAs in Influencing Glioblastoma Multiforme Prognosis. Cells 2024; 13:276. [PMID: 38334668 PMCID: PMC10855153 DOI: 10.3390/cells13030276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/10/2024] Open
Abstract
Glioblastoma multiforme (GBM) is usually treated with surgery followed by adjuvant partial radiotherapy combined with temozolomide (TMZ) chemotherapy. Recent studies demonstrated a better survival and good response to TMZ in methylguanine-DNA methyltransferase (MGMT)-methylated GBM cases. However, approximately 20% of patients with MGMT-unmethylated GBM display an unexpectedly favorable outcome. Therefore, additional mechanisms related to the TMZ response need to be investigated. As such, we decided to investigate the clinical relevance of six miRNAs involved in brain tumorigenesis (miR-181c, miR-181d, miR-21, miR-195, miR-196b, miR-648) as additional markers of response and survival in patients receiving TMZ for GBM. We evaluated miRNA expression and the interplay between miRNAs in 112 IDH wt GBMs by applying commercial assays. Then, we correlated the miRNA expression with patients' clinical outcomes. Upon bivariate analyses, we found a significant association between the expression levels of the miRNAs analyzed, but, more interestingly, the OS curves show that the combination of low miR-648 and miR-181c or miR-181d expressions is associated with a worse prognosis than cases with other low-expression miRNA pairs. To conclude, we found how specific miRNA pairs can influence survival in GBM cases treated with TMZ.
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Affiliation(s)
- Samantha Epistolio
- Laboratory of Genetics and Molecular Pathology, Institute of Pathology, Ente Ospedaliero Cantonale (EOC), 6900 Locarno, Switzerland; (S.E.); (G.D.); (J.B.); (P.S.); (L.M.)
| | - Giulia Dazio
- Laboratory of Genetics and Molecular Pathology, Institute of Pathology, Ente Ospedaliero Cantonale (EOC), 6900 Locarno, Switzerland; (S.E.); (G.D.); (J.B.); (P.S.); (L.M.)
| | - Ismail Zaed
- Service of Neurosurgery, Neurocenter of the Southern Switzerland, Regional Hospital of Lugano, Ente Ospedaliero Cantonale (EOC), 6900 Lugano, Switzerland; (I.Z.); (D.C.); (F.P.); (M.R.); (A.C.); (F.M.)
| | - Nora Sahnane
- Unit of Pathology, Department of Medicine and Technological Innovation, University of Insubria, ASST Sette Laghi, 21100 Varese, Italy; (N.S.); (M.C.); (F.S.)
| | - Debora Cipriani
- Service of Neurosurgery, Neurocenter of the Southern Switzerland, Regional Hospital of Lugano, Ente Ospedaliero Cantonale (EOC), 6900 Lugano, Switzerland; (I.Z.); (D.C.); (F.P.); (M.R.); (A.C.); (F.M.)
| | - Francesco Polinelli
- Service of Neurosurgery, Neurocenter of the Southern Switzerland, Regional Hospital of Lugano, Ente Ospedaliero Cantonale (EOC), 6900 Lugano, Switzerland; (I.Z.); (D.C.); (F.P.); (M.R.); (A.C.); (F.M.)
| | - Jessica Barizzi
- Laboratory of Genetics and Molecular Pathology, Institute of Pathology, Ente Ospedaliero Cantonale (EOC), 6900 Locarno, Switzerland; (S.E.); (G.D.); (J.B.); (P.S.); (L.M.)
| | - Paolo Spina
- Laboratory of Genetics and Molecular Pathology, Institute of Pathology, Ente Ospedaliero Cantonale (EOC), 6900 Locarno, Switzerland; (S.E.); (G.D.); (J.B.); (P.S.); (L.M.)
| | - Federico Mattia Stefanini
- Department of Environmental Science and Policy, Faculty of Science and Technology-ESP, University of Milan, 20122 Milan, Italy;
| | - Michele Cerati
- Unit of Pathology, Department of Medicine and Technological Innovation, University of Insubria, ASST Sette Laghi, 21100 Varese, Italy; (N.S.); (M.C.); (F.S.)
| | - Sergio Balbi
- Division of Neurological Surgery, Department of Biotechnology and Life Sciences, University of Insubria, ASST Sette Laghi, 21100 Varese, Italy;
| | - Luca Mazzucchelli
- Laboratory of Genetics and Molecular Pathology, Institute of Pathology, Ente Ospedaliero Cantonale (EOC), 6900 Locarno, Switzerland; (S.E.); (G.D.); (J.B.); (P.S.); (L.M.)
- Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
| | - Fausto Sessa
- Unit of Pathology, Department of Medicine and Technological Innovation, University of Insubria, ASST Sette Laghi, 21100 Varese, Italy; (N.S.); (M.C.); (F.S.)
| | - Gianfranco Angelo Pesce
- Radiation Oncology, Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale (EOC), 6501 Bellinzona, Switzerland;
| | - Michael Reinert
- Service of Neurosurgery, Neurocenter of the Southern Switzerland, Regional Hospital of Lugano, Ente Ospedaliero Cantonale (EOC), 6900 Lugano, Switzerland; (I.Z.); (D.C.); (F.P.); (M.R.); (A.C.); (F.M.)
- Faculty of Medicine, University of the Southern Switzerland, 6900 Lugano, Switzerland
| | - Andrea Cardia
- Service of Neurosurgery, Neurocenter of the Southern Switzerland, Regional Hospital of Lugano, Ente Ospedaliero Cantonale (EOC), 6900 Lugano, Switzerland; (I.Z.); (D.C.); (F.P.); (M.R.); (A.C.); (F.M.)
| | - Francesco Marchi
- Service of Neurosurgery, Neurocenter of the Southern Switzerland, Regional Hospital of Lugano, Ente Ospedaliero Cantonale (EOC), 6900 Lugano, Switzerland; (I.Z.); (D.C.); (F.P.); (M.R.); (A.C.); (F.M.)
| | - Milo Frattini
- Laboratory of Genetics and Molecular Pathology, Institute of Pathology, Ente Ospedaliero Cantonale (EOC), 6900 Locarno, Switzerland; (S.E.); (G.D.); (J.B.); (P.S.); (L.M.)
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Cani M, Epistolio S, Dazio G, Modesti M, Salfi G, Pedrani M, Isella L, Gillessen S, Vogl UM, Tortola L, Treglia G, Buttigliero C, Frattini M, Pereira Mestre R. Antiandrogens as Therapies for COVID-19: A Systematic Review. Cancers (Basel) 2024; 16:298. [PMID: 38254788 PMCID: PMC10814161 DOI: 10.3390/cancers16020298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND In 2019, the breakthrough of the coronavirus 2 disease (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), represented one of the major issues of our recent history. Different drugs have been tested to rapidly find effective anti-viral treatments and, among these, antiandrogens have been suggested to play a role in mediating SARS-CoV-2 infection. Considering the high heterogeneity of studies on this topic, we decided to review the current literature. METHODS We performed a systematic review according to PRISMA guidelines. A search strategy was conducted on PUBMED and Medline. Only original articles published from March 2020 to 31 August 2023 investigating the possible protective role of antiandrogens were included. In vitro or preclinical studies and reports not in the English language were excluded. The main objective was to investigate how antiandrogens may interfere with COVID-19 outcomes. RESULTS Among 1755 records, we selected 31 studies, the majority of which consisted of retrospective clinical data collections and of randomized clinical trials during the first and second wave of the COVID-19 pandemic. CONCLUSIONS In conclusion, we can state that antiandrogens do not seem to protect individuals from SARS-CoV-2 infection and COVID-19 severity and, thus, their use should not be encouraged in this field.
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Affiliation(s)
- Massimiliano Cani
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland (S.G.); (U.M.V.)
- Oncology Unit, Department of Oncology, University of Turin, S. Luigi Gonzaga Hospital, 10043 Orbassano, Italy;
| | - Samantha Epistolio
- Laboratory of Genetics and Molecular Pathology, Institute of Pathology, Ente Ospedaliero Cantonale (EOC), 6600 Locarno, Switzerland (M.F.)
| | - Giulia Dazio
- Laboratory of Genetics and Molecular Pathology, Institute of Pathology, Ente Ospedaliero Cantonale (EOC), 6600 Locarno, Switzerland (M.F.)
| | - Mikol Modesti
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland (S.G.); (U.M.V.)
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy
| | - Giuseppe Salfi
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland (S.G.); (U.M.V.)
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland
| | - Martino Pedrani
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland (S.G.); (U.M.V.)
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, 20122 Milan, Italy
| | - Luca Isella
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland (S.G.); (U.M.V.)
| | - Silke Gillessen
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland (S.G.); (U.M.V.)
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6900 Lugano, Switzerland;
| | - Ursula Maria Vogl
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland (S.G.); (U.M.V.)
| | - Luigi Tortola
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland (S.G.); (U.M.V.)
| | - Giorgio Treglia
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6900 Lugano, Switzerland;
- Imaging Institute of Southern Switzerland, Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, 1005 Lausanne, Switzerland
| | - Consuelo Buttigliero
- Oncology Unit, Department of Oncology, University of Turin, S. Luigi Gonzaga Hospital, 10043 Orbassano, Italy;
| | - Milo Frattini
- Laboratory of Genetics and Molecular Pathology, Institute of Pathology, Ente Ospedaliero Cantonale (EOC), 6600 Locarno, Switzerland (M.F.)
| | - Ricardo Pereira Mestre
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland (S.G.); (U.M.V.)
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6900 Lugano, Switzerland;
- Clinical Research Unit, myDoctorAngel, 6934 Bioggio, Switzerland
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4
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Bendixen KK, Mindegaard M, Epistolio S, Dazio G, Marchi F, Spina P, Arnspang EC, Soerensen M, Christensen UB, Frattini M, Petersen RK. A qPCR technology for direct quantification of methylation in untreated DNA. Nat Commun 2023; 14:5153. [PMID: 37620381 PMCID: PMC10449789 DOI: 10.1038/s41467-023-40873-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
DNA methylation is important for gene expression and alterations in DNA methylation are involved in the development and progression of cancer and other major diseases. Analysis of DNA methylation patterns has until now been dependent on either a chemical or an enzymatic pre-treatment, which are both time consuming procedures and potentially biased due to incomplete treatment. We present a qPCR technology, EpiDirect®, that allows for direct PCR quantification of DNA methylations using untreated DNA. EpiDirect® is based on the ability of Intercalating Nucleic Acids (INA®) to differentiate between methylated and unmethylated cytosines in a special primer design. With this technology, we develop an assay to analyze the methylation status of a region of the MGMT promoter used in treatment selection and prognosis of glioblastoma patients. We compare the assay to two bisulfite-relying, methyl-specific PCR assays in a study involving 42 brain tumor FFPE samples, revealing high sensitivity, specificity, and the clinical utility of the method.
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Affiliation(s)
- Kamilla Kolding Bendixen
- PentaBase A/S, Odense, Denmark.
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark.
| | | | - Samantha Epistolio
- Laboratory of Molecular Pathology, Institute of Pathology, Ente Ospedaliero Cantonale (EOC), Locarno, Switzerland
| | - Giulia Dazio
- Laboratory of Molecular Pathology, Institute of Pathology, Ente Ospedaliero Cantonale (EOC), Locarno, Switzerland
| | - Francesco Marchi
- Service of Neurosurgery, Neurocenter of the Southern Switzerland, Regional Hospital of Lugano, Lugano, Switzerland
| | - Paolo Spina
- Laboratory of Molecular Pathology, Institute of Pathology, Ente Ospedaliero Cantonale (EOC), Locarno, Switzerland
- Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | - Eva C Arnspang
- Department of Green Technology, University of Southern Denmark, Odense, Denmark
| | - Mette Soerensen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | | | - Milo Frattini
- Laboratory of Molecular Pathology, Institute of Pathology, Ente Ospedaliero Cantonale (EOC), Locarno, Switzerland
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Sørensen AL, Guldmann-Christensen M, Børgesen M, Petersen RK, Flugt K, Duelund JMH, Kyneb MH, Lorenzen J, Pipó-Ollé E, Epistolio S, Riva A, Dazio G, Merlo E, Meyer T, Christensen UB, Frattini M. Detection of BRAF mutations in malignant melanoma and colorectal cancer by SensiScreen® FFPE BRAF qPCR assay. PLoS One 2023; 18:e0281558. [PMID: 36758042 PMCID: PMC9910728 DOI: 10.1371/journal.pone.0281558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/26/2023] [Indexed: 02/10/2023] Open
Abstract
Mutations in BRAF exon 15 lead to conformational changes in its activation loops, resulting in constitutively active BRAF proteins which are implicated in the development of several human cancer types. Different BRAF inhibitors have been developed and introduced in clinical practice. Identification of BRAF mutations influences the clinical evaluation, treatment, progression and for that reason a sensitive and specific identification of BRAF mutations is on request from the clinic. Here we present the SensiScreen® FFPE BRAF qPCR Assay that uses a novel real-time PCR-based method for BRAF mutation detection based on PentaBases proprietary DNA analogue technology designed to work on standard real-time PCR instruments. The SensiScreen® FFPE BRAF qPCR Assay displays high sensitivity, specificity, fast and easy-to-use. The SensiScreen® FFPE BRAF qPCR Assay was validated on two different FFPE tumour biopsy cohorts, one cohort included malignant melanoma patients previously analyzed by the Cobas® 4800 BRAF V600 Mutation Test, and one cohort from colorectal cancer patients previously analyzed by mutant-enriched PCR and direct sequencing. All BRAF mutant malignant melanoma patients were confirmed with the SensiScreen® FFPE BRAF qPCR Assay and additional four new mutations in the malignant melanoma cohort were identified. All the previously identified BRAF mutations in the colorectal cancer patients were confirmed, and additional three new mutations not identified with direct sequencing were detected. Also, one new BRAF mutation not previously identified with ME-PCR was found. Furthermore, the SensiScreen® FFPE BRAF qPCR Assay identified the specific change in the amino acid. The SensiScreen® FFPE BRAF qPCR Assay will contribute to a more specific, time and cost saving approach to better identify and characterize mutations in patients affected by cancer, and consequently permits a better BRAF characterization that is fundamental for therapy decision.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Samantha Epistolio
- Institute of Pathology EOC, Ente Ospedaliero Cantonale, Locarno, Switzerland
| | - Alice Riva
- Institute of Pathology EOC, Ente Ospedaliero Cantonale, Locarno, Switzerland
| | - Giulia Dazio
- Institute of Pathology EOC, Ente Ospedaliero Cantonale, Locarno, Switzerland
| | - Elisabetta Merlo
- Institute of Pathology EOC, Ente Ospedaliero Cantonale, Locarno, Switzerland
| | - Tine Meyer
- Department of Pathology, Laboratory of Research and Development, Aarhus University Hospital, Aarhus, Denmark
| | | | - Milo Frattini
- Institute of Pathology EOC, Ente Ospedaliero Cantonale, Locarno, Switzerland
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